CeleScope Report

Chemistry : For more information, see here.

Raw Reads : Total reads from FASTQ files.

Valid Reads : Reads pass filtering(filtered: reads without poly T, reads without linker, reads without correct barcode or low quality reads).

Q30 of Barcodes : Percent of barcode base pairs with quality scores over Q30.

Q30 of UMIs : Percent of UMI base pairs with quality scores over Q30.

Reads Mapped To Any V(D)J Gene : Fraction of reads that partially or wholly map to any germline V(D)J gene segment.

Reads Mapped To TRA : Fraction of reads that map partially or wholly to a germline TRA gene segment.

Reads Mapped To TRB : Fraction of reads that map partially or wholly to a germline TRB gene segment.

Estimated Number of Cells : The number of barcodes estimated to be associated with cells that express targeted V(D)J transcripts.

Fraction Reads in Cells : Number of reads with cell-associated barcodes divided by the number of reads with valid barcodes.

Mean Reads per Cell : Number of input read pairs divided by the estimated number of cells.

Mean Used Reads per Cell : Mean number of read pairs used in assembly per cell-associated barcode.

Median Used TRA UMIs per Cell : Median number of UMIs assigned to a TRA contig per cell.

Median Used TRB UMIs per Cell : Median number of UMIs assigned to a TRB contig per cell.

Cells With Productive V-J Spanning Pair : Fraction of cell-associated barcodes with at least one productive contig for each chain of the receptor pair.A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.

Cells With Productive V-J Spanning (TRA, TRB) Pair : Fraction of cell-associated barcodes with at least one productive contig for each chain of the (TRA, TRB) receptor pair. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.

Cells With TRA Contig : Fraction of cell-associated barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.

Cells With CDR3-annotated TRA Contig : Fraction of cell-associated barcodes with at least one TRA contig where a CDR3 was detected.

Cells With V-J Spanning TRA Contig : Fraction of cell-associated barcodes with at least one contig spanning the 5' end of the V region to the 3' end of the J region for TRA.

Cells With Productive TRA Contig : Fraction of cell-associated barcodes with at least one contig that spans the 5' end of the V region to the 3' end of the J region for TRA, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the aligned V-J region.

Cells With TRB Contig : Fraction of cell-associated barcodes with at least one TRB contig annotated as a full or partial V(D)J gene.

Cells With CDR3-annotated TRB Contig : Fraction of cell-associated barcodes with at least one TRB contig where a CDR3 was detected.

Cells With V-J Spanning TRB Contig : Fraction of cell-associated barcodes with at least one contig spanning the 5' end of the V region to the 3' end of the J region for TRB.

Cells With Productive TRB Contig : Fraction of cell-associated barcodes with at least one contig that spans the 5' end of the V region to the 3' end of the J region for TRB, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the aligned V-J region.

Cells Match with ScRNA-seq Analysis : The intersection between VDJ cell barcodes and scRNA-Seq barcodes. All the following metrics are based on this intersection.